markophylo: Markov Chain Models for Phylogenetic Trees
Allows for fitting of maximum likelihood models using Markov chains
on phylogenetic trees for analysis of discrete character data. Examples of such
discrete character data include restriction sites, gene family presence/absence,
intron presence/absence, and gene family size data. Hypothesis-driven user-
specified substitution rate matrices can be estimated. Allows for biologically
realistic models combining constrained substitution rate matrices, site rate
variation, site partitioning, branch-specific rates, allowing for non-stationary
prior root probabilities, correcting for sampling bias, etc. See Dang and Golding
(2016) <doi:10.1093/bioinformatics/btv541> for more details.
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